Metabolomics Python Packages

pyopenms

The codebase of the OpenMS project

matchms

Python library for processing (tandem) mass spectrometry data and for computing spectral similarities.

nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

pyopls

A Python 3 implementation of orthogonal projection to latent structures

msbuddy

a python package for molecular formula analysis in MS-based small molecule studies

depthcharge-ms

A deep learning toolkit for mass spectrometry

metbit

Metbit is an python package to analyse metabolomics

isocor

IsoCor: Isotope Correction for mass spectrometry labeling experiments

ultrams

UltraMS pretrained MS/MS models, PyTorch fine-tuning, and pretraining code

spxtacular

Chainable Spectrum API for MS processing: denoising, isotope deconvolution, matching, scoring, plotting

multinmrfit

MultiNMRFit: A software to fit 1D and pseudo-2D NMR spectra

pymultiomics

Python toolbox for multi-omics data mapping and analysis

corems

CoreMS is a comprehensive mass spectrometry software framework

pygoslin

Python implementation of parsers for the Grammars on succinct lipid nomenclature (Goslin).

msi-recal

Cloud engine and platform for metabolite annotation for imaging mass spectrometry

metaspace2020

Cloud engine and platform for metabolite annotation for imaging mass spectrometry

ms-mint

Python library for large-scale targeted metabolomics.

pyqms

pyQms, generalized, fast and accurate mass spectrometry data quantification

mbpls

(Multiblock) Partial Least Squares Regression for Python

dimet

Differential analysis of targeted Isotope-labeled Metabolomics data

ms-mint-app

Web-based post-processing tool for LC-MS metabolomics data. Extract, visualize, and analyze targeted metabolites with interactive browser-based interface.

dimepy

Python package for the high-throughput nontargeted metabolite fingerprinting of nominal mass direct injection mass spectrometry directly from mzML files.

mwtab

The mwtab package is a Python library that facilitates reading and writing files in mwTab format used by the Metabolomics Workbench for archival of Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) experimental data.

sspa

Single sample pathway analysis tools for omics data